Building in-silico pathway SBML models from heterogeneous sources

8th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2008

Volumn , Issue , 2008, Pages

  Kanaris, I ^b   Moutselos, K ^b   Chatziioannou, A ^a   Maglogiannis, I ^c   Kolisis, F N ^a  

^a INSTITUTE OF BIOLOGY   (Greece)

^b UNIVERSITY OF THE AEGEAN   (Greece)

^c UNIVERSITY OF CENTRAL GREECE   (Greece)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMATIC SIMULATION; BIOCHEMICAL PATHWAY; BIOLOGICAL DATA; BIOLOGICAL DATABASE; BIOLOGICAL PROBLEMS; CURATION; HETEROGENEOUS SOURCES; HIGH THROUGHPUT; IN-SILICO; IN-SILICO MODELS; LIFE-SCIENCE; MEASURING TECHNIQUE; METABOLIC PATHWAYS; SOFTWARE SOLUTION; SYSTEMS BIOLOGY; SYSTEMS BIOLOGY MARKUP LANGUAGES;

BIOINFORMATICS; HYPERTEXT SYSTEMS; LINGUISTICS; QUERY LANGUAGES;

MARKUP LANGUAGES;

EID: 67649128734     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BIBE.2008.4696730     Document Type: Conference Paper

References (12)

1. M. Hucka, et.al., "The Systems biology markup language (SBML): a medium for representation and exchange of biochemical network models", Bioinformatics 19: 524-531.
2. Cuellar, Autumn A., Lloyd, Catherine M., Nielsen, Poul F., Bullivant, David P., Nickerson, David P., Hunter, Peter J., "An Overview of CellML 1.1, a Biological Model Description Language", SIMULATION 2003 79: 740-747.
3. Finney A, et. al., "Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions", 2003; Available from: http://sbml.org/specifications/sbml-level-2/version-lmtml/sbml- level-2.html.
4. Schilstra, M.J., "Conversion of CellML 1.1 into SBML L2vl" 2004 http://sbml.org/sofrware/cellml2sbml/conversionof-CellML2SBML. pdf
5. Akira Funahashi, Mineo Morohashi, Hiroaki Kitano, Naoki Tanimura, "CellDesigner: a process diagram editor for gene-regulatory and biochemical networks", BIOSILICO Volume 1, Issue 5, 5 November 2003, Pages 159-162.
6. Mendes P., "Biochemistry by numbers: simulation of biochemical pathways with Gepasi 3", 1997, Trends Biochem Sci 22(9):361-3.
7. Hoops S, Sahle S, Gauges R, Lee C, Pahle J, Simus N, Singhal M, Xu L, Mendes P, Kummer U., "COPASI - a COmplex PAthway Simulator", 2006, Bioinformatics.
8. Rodriguez N, Donizelli M, Le Novère N., "SBMLeditor: effective creation of models in the Systems Biology Markup Language (SBML)", BMC Bioinformatics. 2007 Mar 6; 8:79.
9. A. Funahashi and H. Kitano, "Converting KEGG DB to SBML," Bioinformatics, 2003. 6.
10. Bornstein, B. J., Keating, S. M., Jouraku, A., and Hucka M., "LibSBML: An API Library for SBML", 2008, Bioinformatics, 24(6):880-881
11. M. Hucka, A. Finney, H. M. Sauro H. Bolouri, J. Doyle, H. Kitano, "The ERATO Systems Biology Workbench: Enabling interaction and exchange between software tools for Computational Biology", 2002, Pacific Symposium on Biocomputing 7:450-461
12. Ander, M. Beltrao, P. Di Ventura, B. Ferkinghoff-Borg, J. Foglierini, M. Kaplan, A. Lemerle, C. Tomas-Oliveira, I. Serrano, L., "SmartCell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localization: analysis of simple networks"